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Yorodumi- EMDB-24363: Methanococcus maripaludis chaperonin complex in open conformation -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24363 | |||||||||||||||
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Title | Methanococcus maripaludis chaperonin complex in open conformation | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | Methanococcus maripaludis (archaea) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||||||||
Authors | Zhao Y / Schmid M / Frydman J / Chiu W | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Nat Commun / Year: 2021 Title: CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin. Authors: Yanyan Zhao / Michael F Schmid / Judith Frydman / Wah Chiu / Abstract: Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism ...Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24363.map.gz | 78.3 MB | EMDB map data format | |
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Header (meta data) | emd-24363-v30.xml emd-24363.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_24363.png | 57 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24363 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24363 | HTTPS FTP |
-Related structure data
Related structure data | 7rakMC 7r9eC 7r9hC 7r9iC 7r9jC 7r9kC 7r9mC 7r9oC 7r9uC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10770 (Title: Cryo-EM reveals the stochastic nature of individual ATP binding events in a group II chaperonin Data size: 48.4 Data #1: aligned particle image [picked particles - single frame - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24363.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Ternary complex of chaperonin MmCpn in open state under ATP condition
Entire | Name: Ternary complex of chaperonin MmCpn in open state under ATP condition |
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Components |
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-Supramolecule #1: Ternary complex of chaperonin MmCpn in open state under ATP condition
Supramolecule | Name: Ternary complex of chaperonin MmCpn in open state under ATP condition type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Methanococcus maripaludis (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 1 MDa |
-Macromolecule #1: Chaperonin
Macromolecule | Name: Chaperonin / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: Methanococcus maripaludis (archaea) |
Molecular weight | Theoretical: 54.560789 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGRDAQRMNI LAGRIIAETV RSTLGPKGMD KMLVDDLGDV VVTNDGVTIL REMSVEHPAA KMLIEVAKTQ EKEVGDGTTT AVVVAGELL RKAEELLDQN VHPTIVVKGY QAAAQKAQEL LKTIACEVGA QDKEILTKIA MTSITGKGAE KAKEKLAEII V EAVSAVVD ...String: MGRDAQRMNI LAGRIIAETV RSTLGPKGMD KMLVDDLGDV VVTNDGVTIL REMSVEHPAA KMLIEVAKTQ EKEVGDGTTT AVVVAGELL RKAEELLDQN VHPTIVVKGY QAAAQKAQEL LKTIACEVGA QDKEILTKIA MTSITGKGAE KAKEKLAEII V EAVSAVVD DEGKVDKDLI KIEKKSGASI DDTELIKGVL VDKERVSAQM PKKVTDAKIA LLNCAIEIKE TETDAEIRIT DP AKLMEFI EQEEKMLKDM VAEIKASGAN VLFCQKGIDD LAQHYLAKEG IVAARRVKKS DMEKLAKATG ANVITNIKDL SAQ DLGDAG LVEERKISGD SMIFVEECKH PKAVTMLIRG TTEHVIEEVA RAVDDAVGVV GCTIEDGRIV SGGGSTEVEL SMKL REYAE GISGREQLAV RAFADALEVI PRTLAENAGL DAIEILVKVR AAHASNGNKC AGLNVFTGAV EDMCENGVVE PLRVK TQAI QSAAESTEML LRIDDVIAAE KLR |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 16 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160000 |